Contacts of the helix formed by residues 293 - 309 (chain I) in PDB entry 1SXG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 293 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I ILE* 3.9 12.1 - - + -
291I VAL* 3.8 17.0 - - + +
292I GLN* 1.3 79.7 - - + +
294I MET* 1.3 65.1 + - - +
295I TYR* 3.1 3.6 - - - -
296I ASP* 3.0 26.8 + - + +
297I ILE* 2.9 23.1 + - + +
321I LEU* 4.2 19.1 - - + -
322I PRO 3.8 23.3 - - - +
324I ARG* 5.7 2.7 - - - +
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Residues in contact with MET 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I PHE* 3.5 37.0 - - + -
77I GLU* 3.8 42.4 - - + +
78I LEU* 3.8 30.3 - - + +
81I GLY* 5.6 3.5 - - - -
275I ASP 3.8 11.0 - - - +
276I ASN 3.6 23.3 - - - +
277I THR* 4.1 3.4 - - - -
292I GLN* 2.7 19.0 + - + +
293I PRO* 1.3 69.0 - - - +
295I TYR* 1.3 61.8 + - - +
297I ILE* 3.4 9.7 + - + +
298I GLY* 3.1 18.7 + - - -
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Residues in contact with TYR 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I GLY* 4.7 17.3 - - - -
84I ASP* 4.9 9.8 - - + -
85I ILE* 3.2 33.4 - - + +
88I MET* 4.6 14.4 - - - +
293I PRO 3.0 1.0 + - - -
294I MET* 1.3 75.7 - - - +
296I ASP* 1.3 79.5 + - - +
298I GLY* 3.1 2.5 + - - -
299I ALA* 2.8 31.7 + - + +
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Residues in contact with ASP 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I PRO* 3.0 27.1 + - + +
295I TYR* 1.3 86.7 - - - +
297I ILE* 1.3 52.2 + - - +
299I ALA* 3.3 6.8 - - - +
300I VAL* 2.7 41.4 + - + +
321I LEU* 3.8 21.9 - - + +
322I PRO* 6.2 0.3 - - - +
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Residues in contact with ILE 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I PHE* 5.6 0.2 - - + -
78I LEU* 4.6 8.5 - - + -
145I ALA* 4.0 19.1 - - + -
146I ALA* 4.2 18.2 - - + +
157I VAL* 3.5 34.6 - - + +
158I THR* 4.7 2.7 - - - +
159I ILE* 4.6 9.6 - - + -
292I GLN* 4.0 27.1 - - + +
293I PRO* 2.9 20.2 + - + +
294I MET* 3.6 11.2 - - + +
296I ASP* 1.3 73.4 - - - +
298I GLY* 1.3 66.2 + - - +
301I ALA* 2.9 23.7 + - - +
321I LEU* 3.7 14.8 - - + -
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Residues in contact with GLY 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 4.5 0.6 - - - +
81I GLY 5.5 0.2 - - - -
82I ILE* 3.4 32.7 - - - +
85I ILE* 4.1 11.7 - - - -
294I MET 3.1 14.7 + - - -
295I TYR* 3.7 2.2 - - - -
297I ILE* 1.3 74.1 - - - +
299I ALA* 1.3 64.7 + - - +
301I ALA* 3.0 2.7 + - - +
302I MET* 2.8 27.7 + - - +
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Residues in contact with ALA 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I ILE* 3.9 23.9 - - + +
89I TYR* 4.1 3.9 + - - -
295I TYR* 2.8 22.7 + - + +
296I ASP* 3.3 13.7 - - - +
298I GLY* 1.3 74.4 - - - +
300I VAL* 1.3 60.3 + - + +
302I MET* 3.4 2.8 + - - +
303I ARG* 3.0 27.8 + - - +
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Residues in contact with VAL 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I VAL* 4.0 23.1 - - + -
296I ASP* 2.7 25.3 + - + +
299I ALA* 1.3 72.1 - - + +
301I ALA* 1.3 61.0 + - - +
303I ARG* 3.6 14.3 - - - +
304I LEU* 2.9 34.0 + - + +
319I VAL* 4.3 22.4 - - + -
321I LEU* 4.1 22.0 - - + -
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Residues in contact with ALA 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I ILE* 4.2 17.3 - - + -
143I VAL* 3.9 14.2 - - + +
145I ALA* 4.6 9.6 - - + -
157I VAL* 3.3 20.4 - - + +
297I ILE 2.9 19.5 + - - +
298I GLY* 3.6 5.8 - - - +
300I VAL* 1.3 75.5 - - - +
302I MET* 1.3 55.6 + - - +
304I LEU* 3.3 5.6 + - - +
305I LEU* 2.7 34.5 + - - +
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Residues in contact with MET 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 4.0 15.5 - - + -
82I ILE* 4.7 13.5 - - + +
85I ILE* 3.6 31.2 - - + -
86I ALA* 4.6 10.5 - - - -
89I TYR* 4.2 8.5 - - + -
91I TYR* 3.8 28.0 - - + -
121I ILE* 3.3 33.9 - - + -
298I GLY 2.8 15.2 + - - +
299I ALA 3.8 3.8 - - - +
301I ALA* 1.3 72.3 - - - +
303I ARG* 1.3 58.7 + - - +
305I LEU* 3.0 18.3 + - + +
306I THR* 2.6 40.6 + - - -
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Residues in contact with ARG 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I TYR* 3.6 15.4 + - - +
299I ALA 3.0 18.2 + - - +
300I VAL* 3.6 16.2 - - - +
302I MET* 1.3 76.2 - - - +
304I LEU* 1.3 71.3 + - - +
306I THR* 3.2 5.1 + - - -
307I LYS* 3.1 65.7 + - + +
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Residues in contact with LEU 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I VAL* 4.1 12.6 - - + -
155I PRO* 3.8 19.3 - - + -
156I SER 4.4 3.4 - - - +
157I VAL* 5.0 6.3 - - + -
300I VAL* 2.9 23.2 + - + +
301I ALA* 3.4 5.2 - - - +
303I ARG* 1.3 84.3 - - - +
305I LEU* 1.3 61.1 + - - +
307I LYS* 3.2 16.5 + - + +
308I TYR* 2.9 34.8 + - + -
314I VAL* 4.4 7.9 - - + -
316I SER* 3.5 22.4 - - - +
317I SER 3.4 22.4 - - - +
319I VAL* 4.5 15.3 - - + -
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Residues in contact with LEU 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 3.8 11.7 - - + -
119I GLY* 3.9 4.5 - - - -
120I ILE 3.8 7.9 - - - +
121I ILE* 3.2 26.5 - - + -
141I PRO* 3.4 38.1 - - + +
143I VAL* 3.6 20.6 - - + +
301I ALA 2.7 21.0 + - - +
302I MET* 3.4 17.9 - - + +
304I LEU* 1.3 69.7 - - - +
306I THR* 1.3 67.4 + - - +
308I TYR* 3.1 5.0 + - + +
309I MET* 2.8 45.5 + - + +
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Residues in contact with THR 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I TYR* 3.6 16.7 - - + -
91I TYR* 2.5 32.7 + - - +
302I MET 2.6 21.6 + - - -
303I ARG* 3.2 5.8 + - - -
305I LEU* 1.3 72.6 - - - +
307I LYS* 1.3 65.1 + - + +
309I MET* 3.1 10.6 + - + -
310I ASN* 3.1 37.7 + - - +
312I GLU* 5.6 2.0 - - - +
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Residues in contact with LYS 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303I ARG* 3.1 48.1 + - + +
304I LEU* 3.5 9.0 - - + +
305I LEU 3.2 0.4 - - - -
306I THR* 1.3 78.6 - - + +
308I TYR* 1.3 57.2 + - - +
310I ASN* 2.9 17.0 + - - -
312I GLU* 3.0 51.9 + - + +
313I THR 2.8 29.5 + - - -
314I VAL* 3.8 25.0 - - + +
315I ASP* 4.8 8.9 + - - +
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Residues in contact with TYR 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I PRO* 3.4 34.0 - - + +
142I VAL 6.0 0.4 - - - -
143I VAL* 5.1 3.1 - - + -
155I PRO* 3.4 39.2 - - + +
304I LEU* 2.9 38.1 + - + -
305I LEU* 3.1 6.7 + - - +
307I LYS* 1.3 72.2 - - - +
309I MET* 1.3 59.0 + - - +
310I ASN 2.8 9.4 + - - -
311I LYS* 3.4 13.2 + - - +
312I GLU 5.1 3.1 - - - -
314I VAL* 3.7 34.1 - - + +
317I SER* 3.9 12.0 + - - -
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Residues in contact with MET 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I THR* 4.0 10.8 - - + -
63I VAL* 5.1 2.5 - - + -
91I TYR* 3.9 26.7 - - + +
118I ASP* 3.6 48.0 - - + +
119I GLY* 4.0 3.6 - - - -
141I PRO* 4.1 9.4 - - + -
302I MET* 5.1 0.2 - - + -
305I LEU* 2.8 46.7 + - + +
306I THR* 3.1 16.8 + - + +
308I TYR* 1.3 74.7 - - - +
310I ASN* 1.3 71.6 + - - +
311I LYS* 3.8 8.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il